Module information
Details
- Title
- Solid Cancers 1
- Type
- Specialist
- Module code
- S-CG-S1-2
- Credits
- 10
- Requirement
- Compulsory
Aim of this module
This module will provide the trainees with an introduction of molecular mechanisms leading to the development of solid cancers and the associated genomic testing. This module will focus on patients with colorectal cancer, melanoma, and lung cancer as exemplars, and will provide trainees with the knowledge to understand the organisation and delivery of a diagnostic cancer genomic service. This module will provide trainees with the skills to recognise the sample diagnostic pathway, the relevant testing strategies including NGS and non-NGS assays, as well as the importance of bioinformatic/NGS quality metrics. This module will provide the trainees with the skills to analyse and interpret patient results, and the requirements for additional investigations.
Work-based content
Competencies
| # | Learning outcome | Competency | Action |
|---|---|---|---|
| # 1 | Learning outcome 1 |
Competency
Receive samples and referral information for a range of solid cancers, to include:
|
Action View |
| # 2 | Learning outcome 2 |
Competency
Select the laboratory molecular assay for patients referred for solid tumour investigation for:
|
Action View |
| # 3 | Learning outcome 2,3 |
Competency
Analyse and interpret molecular laboratory assays (non-NGS) applicable to solid tumour referrals |
Action View |
| # 4 | Learning outcome 5 |
Competency
Perform at least one quality measure for an NGS assay, and assess all quality measures from initiation to sequencing |
Action View |
| # 5 | Learning outcome 3,4,5 |
Competency
Analyse and interpret DNA and RNA NGS data for sequence variants (SNV, SV), copy number variants (CNV) and fusion genes where applicable for:
|
Action View |
| # 6 | Learning outcome 3,4,5 |
Competency
Perform variant interpretations for:
|
Action View |
| # 7 | Learning outcome 3,4,5,6 |
Competency
Prepare a range of interpretative reports for colorectal referrals |
Action View |
| # 8 | Learning outcome 3,4,5,6 |
Competency
Prepare a range of interpretative reports for melanoma referrals |
Action View |
| # 9 | Learning outcome 3,4,5,6 |
Competency
Prepare a range of interpretative reports for lung referrals |
Action View |
| # 10 | Learning outcome 3,4,6 |
Competency
Assist with the preparation of cases to be discussed and reviewed in a multidisciplinary team meeting or tumour board meeting with other healthcare professionals |
Action View |
Assessments
Complete 2 Case-Based Discussions
Complete 2 DOPS or OCEs
Direct Observation of Practical Skills Titles
- Perform morphological assessment for colorectal or lung cancer, or melanoma
- Perform tumour genotype analysis using bioinformatic pipelines and associated tools for colorectal or lung cancer, or melanoma
- Produce a diagnostic clinical report for a patient with hotspot mutation(s) for colorectal or lung cancer, or melanoma
- Interpret a molecular assay (non NGS) for colorectal or lung cancer, or melanoma
- Interpret a somatic variant, discuss the relevance for diagnosis for colorectal or lung cancer, or melanoma
- Interpret a germline variant, discuss the relevance for diagnosis for colorectal or lung cancer, or melanoma
Observed Communication Event Titles
- Advise another healthcare professional on the appropriate acceptance criteria for a sample for investigation for solid cancers
- Inform another healthcare professional of a delay in results or a need for additional or confirmatory testing for colorectal or lung cancer, or melanoma
Learning outcomes
| # | Learning outcome |
|---|---|
| 1 | Apply the appropriate sample acceptance criteria in terms of cellularity, necrosis and tumour burden in the context of downstream testing for solid cancers. |
| 2 | Select the relevant testing strategy for patients referred for diagnostic genomic testing for colorectal and lung cancer, and melanoma. |
| 3 | Analyse, interpret and prepare interpretive reports of clinically relevant findings for patients with colorectal and lung cancer, and melanoma. |
| 4 | Evaluate the clinical significance of variants identified for colorectal and lung cancer, and melanoma using a range of bioinformatics tools following best practice guidelines. |
| 5 | Interpret the bioinformatic and NGS quality metrics in relation to assay performance and EQA. |
| 6 | Practice with relevant specialties for the diagnosis and treatment of cancer patients and contribute to multidisciplinary team meetings |
Academic content (MSc in Clinical Science)
Important information
The academic parts of this module will be detailed and communicated to you by your university. Please contact them if you have questions regarding this module and its assessments. The module titles in your MSc may not be exactly identical to the work-based modules shown in the e-portfolio. Your modules will be aligned, however, to ensure that your academic and work-based learning are complimentary.
Learning outcomes
On successful completion of this module the trainee will be able to:
- Apply integrative knowledge of the aetiology and biological processes leading to the development solid cancer, including colorectal and lung cancer, and melanoma.
- Describe the genomic mechanisms underpinning the development of solid cancers, including colorectal and lung cancer, and melanoma.
- Critically evaluate utilisation of genomic testing in acquired colorectal cancer compared with inherited disease with specific reference to diagnosis, prognosis, monitoring and treatment.
- Explain the appropriate technologies and their application to the analysis of solid cancers, including colorectal and lung cancer, and melanoma, to include reflex testing.
- Apply integrative knowledge of patient pathway for solid cancers from sampling to reporting of laboratory findings and feedback of results, including colorectal and lung cancer, and melanoma
- Evaluate the appropriate therapeutics, inhibitors or other appropriate therapies to guide patient disease management depending on the clinical status such as metastases and genomic results.
Indicative content
- Aetiology of colorectal and lung cancer, and melanoma.
- Molecular basis and underlying mechanisms, including epigenetics, driver and passenger mutations, oncogenes and tumour suppressor genes, signalling pathways and associated genes.
- Mechanisms of genomic aberrations in colorectal and lung cancer, and melanoma including relapse, metastasis, and resistance and secondary mutations.
- Associated genomic aberrations and role within diagnosis, prognosis and disease management.
- Current nomenclature used to describe genomic alterations.
- Germline associations.
- Germline and somatic variant interpretation.
- Current laboratory techniques and methodologies employed for tumour genotyping (e.g. extraction, polymerase chain reaction, and sequencing technologies)
- Bespoke assays/in-house.
- Commercially available kits.
- Histopathological sample processing requirements for genotyping and impact on upstream testing.
- Nucleic acid extraction methodologies.
- Analytical and clinical sensitivity and specificity of these tests, including limits of detection (LOD).
- Understanding the significance of low-level variants in the clinical context.
- The use of bioinformatics tools and relevant genomic databases.
- Quality control, validation and verification, and external quality assessment schemes.
- Standardisation and the use of appropriate tools and nomenclature for reporting variants.
- Potential application of relevant emerging technologies (e.g. digital pathology).
- Genomic aberrations seen in colorectal and lung cancer, and melanoma and their role in disease management in the context of their predictive and prognostic value.
- Application of current therapeutics to the clinical scenario.
- Modern sequencing technologies employed and troubleshooting, including panel based testing and whole genome analysis using both DNA and RNA as analytes.
- Precision medicine e.g. the role of tyrosine kinase inhibitors, detection of hotspot mutations (such as EGFR), intracellular signalling targeted therapy (such as RAS, BRAF), translocated genes targets (such as ALK, ROS1, NTRK) in lung cancer and the role of PARP inhibitors in ovarian cancers.
- Therapeutics available for primary and secondary disease and how these are used in the clinical setting.
- Clinical trials and their role in the diagnostic setting.
- Multidisciplinary team working, including pathology, histopathology, genomics laboratory, clinical genetics and disease specific multidisciplinary teams.
- Impact of genomics on patients and their families including ethical considerations, including consent.
- Best practice guidelines, including national guidance, clinical trials, advisory and regulatory bodies, NICE guidance and standard of care testing.
- Horizon scanning for example tumour mutation burden, WGS, and future biomarkers.
Clinical experiences
Important information
Clinical experiential learning is the range of activities trainees may undertake in order to gain the experience and evidence to demonstrate their achievement of module competencies and assessments. The list is not definitive or mandatory, but training officers should ensure, as best training practice, that trainees gain as many of these clinical experiences as possible. They should be included in training plans, and once undertaken they should support the completion of module assessments and competencies within the e-portfolio.
Activities
- Observe the histopathological preparation of samples to appreciate the impact on onward molecular analysis.
- Observe NGS laboratory procedures for cancer gene panels applicable to solid cancer referrals to appreciate the workflow. Attend a national group/tumour board meeting.